Contacts of the helix formed by residues 29 - 53 (chain A) in PDB entry 2O36
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASP 3.7 1.0 + - - -
28A LEU* 1.3 75.4 - - - +
30A ALA* 1.3 67.0 + - - +
31A GLN* 3.5 9.6 + - - +
32A GLN* 2.8 36.3 + - - +
33A ILE* 3.0 23.5 + - - +
94A ILE* 4.3 8.3 - - - -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 1.3 74.3 - - - +
31A GLN* 1.3 62.6 + - - +
33A ILE* 3.4 6.8 + - - +
34A GLU* 3.1 22.3 + - - +
93A ASP* 3.6 37.2 - - + +
94A ILE* 4.0 8.4 - - + +
97A ALA* 3.8 18.1 - - + +
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 3.1 9.4 + - - +
30A ALA* 1.3 76.1 - - - +
32A GLN* 1.3 62.8 + - + +
34A GLU* 3.3 15.1 + - - +
35A GLU* 3.0 55.9 + - + +
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 4.8 7.9 - - - +
27A ASP* 3.4 6.6 + - - +
28A LEU* 3.0 35.8 - - + +
29A SER* 2.8 38.4 + - - +
31A GLN* 1.3 75.3 - - + +
33A ILE* 1.3 60.0 + - - +
35A GLU* 3.8 11.6 - - - +
36A ARG* 2.8 41.0 + - + +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.4 14.8 - - + +
29A SER 3.0 17.0 + - - +
30A ALA* 3.5 7.9 - - - +
31A GLN 3.2 0.2 - - - -
32A GLN* 1.3 77.6 - - - +
34A GLU* 1.3 58.3 + - - +
36A ARG* 4.8 0.2 - - - +
37A THR* 2.8 33.6 + - - -
81A ILE 5.9 0.2 - - - +
82A LEU* 3.9 24.5 - - + +
85A PRO* 4.5 9.9 - - + -
94A ILE* 3.8 39.9 - - + +
97A ALA* 3.7 27.8 - - + +
98A SER* 4.2 10.3 - - - +
101A ALA* 3.9 15.3 - - + -
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 3.1 10.2 + - - +
31A GLN* 3.3 17.6 + - - +
33A ILE* 1.3 84.3 - - - +
35A GLU* 1.3 61.9 + - - +
37A THR* 3.4 5.7 + - - -
38A ARG* 3.1 55.8 + - - +
97A ALA* 5.8 3.1 - - + -
101A ALA* 6.0 0.4 - - - -
104A LYS* 6.0 4.7 - - - +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.0 54.9 + - + +
32A GLN* 3.8 8.7 + - - +
34A GLU* 1.3 74.8 - - - +
36A ARG* 1.3 67.2 + - + +
38A ARG* 3.2 25.5 + - - +
39A GLU* 3.0 40.5 + - - +
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 4.0 24.8 - - - +
28A LEU* 3.0 50.5 - - - +
32A GLN* 2.8 29.1 + - + +
35A GLU* 1.3 73.7 - - + +
37A THR* 1.3 57.4 + - - +
39A GLU* 3.7 12.8 - - - +
40A LEU* 2.8 32.2 + - - +
78A GLN* 3.4 26.1 + - - +
81A ILE* 6.4 0.2 - - - +
82A LEU* 3.8 19.9 - - + +
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE 2.8 21.6 + - - -
34A GLU* 3.6 6.3 - - - -
35A GLU 3.2 0.2 - - - -
36A ARG* 1.3 74.7 - - - +
38A ARG* 1.3 67.0 + - - +
40A LEU* 3.4 2.7 + - - +
41A ILE* 3.0 39.9 + - + +
82A LEU* 3.5 14.2 - - - +
101A ALA* 3.2 29.5 - - + +
104A LYS* 4.2 16.8 - - + -
105A LEU* 3.9 26.0 - - + -
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 3.1 49.8 + - - +
35A GLU* 3.2 30.6 + - - +
37A THR* 1.3 79.3 - - + +
39A GLU* 1.3 59.3 + - + +
41A ILE* 3.4 7.3 + - - +
42A GLU* 3.0 29.5 + - - +
104A LYS* 5.8 11.0 - - + +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.0 38.1 + - - +
36A ARG* 3.7 10.8 + - - +
38A ARG* 1.3 75.2 - - + +
40A LEU* 1.3 60.1 + - - +
42A GLU* 3.2 11.8 + - - +
43A GLN* 2.9 54.4 + - - +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 2.8 22.3 + - - +
37A THR 3.7 4.5 - - - +
39A GLU* 1.3 72.9 - - - +
41A ILE* 1.3 58.3 + - - +
43A GLN* 3.3 9.0 + - + +
44A THR* 2.8 45.2 + - - +
74A THR* 4.7 1.3 - - - +
75A TYR* 3.7 34.5 - - + +
78A GLN* 3.6 42.4 - - + +
79A ARG* 3.8 15.3 - - - +
82A LEU* 4.1 12.6 - - + -
105A LEU* 4.1 6.5 - - + -
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Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 3.0 27.4 + - + +
38A ARG* 3.8 6.3 - - + +
40A LEU* 1.3 75.6 - - - +
42A GLU* 1.3 59.2 + - - +
45A LYS* 2.9 39.7 + - + +
104A LYS* 4.1 23.8 - - + +
105A LEU* 3.6 26.2 - - + -
108A PHE* 3.6 38.4 - - + -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG 3.0 18.0 + - - +
39A GLU* 3.6 11.8 - - - +
41A ILE* 1.3 78.1 - - - +
43A GLN* 1.3 68.0 + - - +
45A LYS* 3.9 5.5 - - - +
46A ARG* 3.1 23.3 + - + +
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Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU* 2.9 46.3 + - - +
40A LEU* 3.8 8.8 - - + +
42A GLU* 1.3 84.1 + - + +
44A THR* 1.3 63.3 + - - +
46A ARG* 3.2 26.6 - - - +
47A VAL* 3.6 10.7 + - - +
71A VAL* 5.7 0.2 - - - -
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 2.8 31.0 + - - +
43A GLN* 1.3 70.4 - - - +
45A LYS* 1.3 67.9 + - - +
47A VAL* 3.0 14.0 + - - +
48A TYR* 3.3 26.5 + - + -
71A VAL* 3.8 25.1 - - + +
74A THR* 5.6 0.5 + - - -
75A TYR* 3.3 28.8 - - + +
108A PHE* 3.7 25.1 - - + -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 2.9 25.1 + - + +
42A GLU* 3.9 6.3 - - - +
44A THR* 1.3 76.0 - - - +
46A ARG* 1.3 56.2 + - - +
48A TYR* 3.2 5.9 + - - +
49A ASP* 2.8 61.9 + - - +
108A PHE* 3.8 22.6 - - + -
111A GLU* 4.5 15.3 - - - +
112A MET* 4.5 8.1 - - + -
115A ARG* 4.6 5.4 - - - +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU* 3.1 13.9 + - + +
43A GLN* 3.2 20.3 - - - +
45A LYS* 1.3 78.6 - - - +
47A VAL* 1.3 57.1 + - - +
49A ASP* 3.5 8.8 + - - +
50A GLN* 3.0 53.3 + - + +
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLN 3.9 10.3 - - - +
44A THR 3.0 7.6 + - - +
46A ARG* 1.3 76.3 - - + +
48A TYR* 1.3 66.7 + - - +
50A GLN* 3.2 17.3 + - + +
51A VAL* 2.9 32.0 + - + +
67A ALA* 4.0 16.6 - - + +
68A LEU* 5.0 2.0 - - + -
71A VAL* 3.8 40.2 - - + -
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Residues in contact with TYR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 3.3 33.9 + - + -
45A LYS 3.2 6.6 + - - +
47A VAL* 1.3 80.8 - - + +
49A ASP* 1.3 53.2 + - - +
51A VAL* 3.2 4.2 + - - -
52A GLY* 2.7 32.2 + - - -
68A LEU* 3.6 27.4 + - + +
71A VAL* 4.1 17.1 - - + +
72A GLU* 5.8 4.2 - - - +
112A MET* 3.7 52.7 - - + +
115A ARG* 3.8 7.8 + - - +
118A VAL* 3.5 27.3 - - + +
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 2.8 48.1 + - - +
46A ARG* 3.6 8.6 - - - +
47A VAL 3.2 0.2 - - - -
48A TYR* 1.3 76.8 - - - +
50A GLN* 1.3 62.1 + - + +
52A GLY* 3.3 0.7 + - - -
53A THR* 2.9 32.3 + - + +
115A ARG* 3.0 32.3 + - - +
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 3.0 52.6 + - + +
47A VAL* 3.4 18.0 - - + +
49A ASP* 1.3 79.7 - - + +
51A VAL* 1.3 62.7 + - + +
53A THR* 3.4 13.2 + - - -
54A GLN* 3.4 14.7 + - - +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 2.9 22.0 + - + +
48A TYR* 3.7 5.6 - - - +
50A GLN* 1.3 77.2 - - + +
52A GLY* 1.3 62.4 + - - +
53A THR 3.1 1.6 + - - -
54A GLN* 3.1 32.6 - - - +
63A SER 4.0 18.6 - - - +
64A THR* 4.2 15.5 - - + +
67A ALA* 4.1 14.8 - - + -
68A LEU* 4.3 17.9 - - + -
118A VAL* 3.9 22.2 - - + +
121A ARG* 3.2 19.8 - - + +
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR 2.7 20.5 + - - -
49A ASP 3.8 0.7 - - - -
50A GLN 3.3 0.2 - - - -
51A VAL* 1.3 73.2 - - - +
53A THR* 1.3 60.8 + - - +
54A GLN 3.6 0.4 - - - -
117A ASP* 3.3 25.2 - - - +
118A VAL* 3.8 19.7 - - - -
121A ARG* 3.1 24.5 + - - -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 2.9 20.7 + - + +
50A GLN* 3.4 8.5 + - - -
51A VAL 3.1 0.8 - - - -
52A GLY* 1.3 80.2 - - - +
54A GLN* 1.3 67.8 + - - +
55A GLU* 3.6 5.9 + - - +
115A ARG* 5.9 0.2 - - - +
117A ASP* 5.0 4.5 - - - +
121A ARG* 4.0 5.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il